Streams flowing through urban areas receive high pollutant loads from their small drainage areas. Therefore, the water quality of urban streams is generally vary sensitive to the urbanization and the construction of a sewerage system. In this study, we carried out the water quality observation of the Kaki River, which is a typical urban stream flowing through Nagaika City, to investigate the mechanism of water purification in the river. On the basis of the observational results, we proposed a mathematical model to describe BOD, DO and SS in the river.Two important processes of the purification are revealed from repeated observation of the water quality of the river. One is that the settling of the suspended materials is the dominant process of the apparent purification. The other is that the Sediment Oxygen Demand (SOD) affects the oxygen balanc of the river water. Experiments on the SOD were made using core-sampled sediments. The results showed that the SOD is expressed as a product of the sediment BOD and the rate constant which shows an Arrhenius-type dependence on the water temperature.A simulation model was developed to describe BOD, DO and SS in a river. In order to distinguish the settling process separately, the particulate BOD and the dissolved BOD are considered as model variables. The SOD, resuspension of the sediments and release of the dissolved BOD are taken into account as model processes. All model constants including the rate constant of the SOD were evaluated by experiments. The model successfully reproduced the distribution of BOD, SS and DO in the Kaki River.The model analysis confirms that the settling of the particulate matter is the dominant process of the apparent purification in the river. Cleaning of deposited sediments as well as reducing pollutant loads due to sewage construction is effective for the improvement of the water quality in urban streams.